2024
North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic
Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M. North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic. BMC Infectious Diseases 2024, 24: 751. PMID: 39075335, PMCID: PMC11288047, DOI: 10.1186/s12879-024-09658-6.Peer-Reviewed Original ResearchConceptsGenome sequenceCombination of genome sequencingTrace transmission pathwaysDengue virusHistorical climatic patternsHigh climatic suitabilityCo-circulationDengue virus serotype 2Transmission pathwaysPhylogenetic analysisVirus transmission pathwaysBiodiversity hotspotHistorical climate dataVirus lineagesDominican RepublicImpacts of climate changeLineagesClimatic suitabilityClimate dataRising temperaturePathwaySerotype 2Subtropical regionsTransmission dynamicsImpact of climatic factorsTravel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Taylor-Salmon E, Hill V, Paul L, Koch R, Breban M, Chaguza C, Sodeinde A, Warren J, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán J, Santiago G, Adams L, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman F, Galán J, Huits R, Hamer D, Vogels C, Morrison A, Michael S, Grubaugh N. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nature Communications 2024, 15: 3508. PMID: 38664380, PMCID: PMC11045810, DOI: 10.1038/s41467-024-47774-8.Peer-Reviewed Original ResearchMeSH KeywordsCaribbean RegionDengueDengue VirusDisease OutbreaksEpidemiological MonitoringHumansPhylogenySerogroupTravelConceptsDengue virusDENV-3Rates of severe diseaseMosquito-borne viral diseasePublic health threatPattern of spreadSevere diseaseLocal surveillanceGenomic epidemiologyEpidemiological patternsVirus surveillanceSurveillanceHealth threatSerotypesDiseaseIncreased rateDengueViral diseasesVirusInfected travelersFrequent outbreaks
2023
Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi
Walker J, Chaguza C, Grubaugh N, Carey M, Baker S, Khan K, Bogoch I, Pitzer V. Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi. Nature Communications 2023, 14: 6502. PMID: 37845201, PMCID: PMC10579367, DOI: 10.1038/s41467-023-42353-9.Peer-Reviewed Original ResearchConceptsXDR S. TyphiS. typhiDrug-resistant Salmonella enterica serovar TyphiDrug-resistant Salmonella TyphiTyphoid outbreakMajor public health threatResistant Salmonella typhiPublic health activitiesTyphoid fever incidencePublic health threatSalmonella enterica serovar TyphiXDR typhoidEnterica serovar TyphiH58 haplotypeHigh riskOnward transmissionTyphoid feverSignificant associationHealth activitiesFever incidenceHealth threatFuture outbreaksSerovar TyphiSalmonella typhiTyphiDynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States
Hill V, Koch R, Bialosuknia S, Ngo K, Zink S, Koetzner C, Maffei J, Dupuis A, Backenson P, Oliver J, Bransfield A, Misencik M, Petruff T, Shepard J, Warren J, Gill M, Baele G, Vogels C, Gallagher G, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer L, Armstrong P, Ciota A, Grubaugh N. Dynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States. Current Biology 2023, 33: 2515-2527.e6. PMID: 37295427, PMCID: PMC10316540, DOI: 10.1016/j.cub.2023.05.047.Peer-Reviewed Original ResearchToward a global virus genomic surveillance network
Hill V, Githinji G, Vogels C, Bento A, Chaguza C, Carrington C, Grubaugh N. Toward a global virus genomic surveillance network. Cell Host & Microbe 2023, 31: 861-873. PMID: 36921604, PMCID: PMC9986120, DOI: 10.1016/j.chom.2023.03.003.Peer-Reviewed Original Research
2022
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Outbreak at a College With High Coronavirus Disease 2019 (COVID-19) Vaccination Coverage—Connecticut, August 2021–September 2021
Bart S, Curtiss CC, Earnest R, Lobe-Costonis R, Peterson H, McWilliams C, Billig K, Hadler JL, Grubaugh ND, Arcelus VJ, Sosa LE. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Outbreak at a College With High Coronavirus Disease 2019 (COVID-19) Vaccination Coverage—Connecticut, August 2021–September 2021. Clinical Infectious Diseases 2022, 75: s243-s250. PMID: 35675696, PMCID: PMC9214140, DOI: 10.1093/cid/ciac422.Peer-Reviewed Original ResearchMeSH KeywordsConnecticutCOVID-19Disease OutbreaksHumansPhylogenySARS-CoV-2Vaccination CoverageVaccinesConceptsSARS-CoV-2 infectionLaboratory-confirmed SARS-CoV-2 infectionSARS-CoV-2 casesHigh vaccination coverageMultivariate logistic regressionDelta variant outbreakSARS-CoV-2 outbreakVaccine seriesVaccination historyVaccination coverageUnvaccinated studentsViral testsVariant outbreakInfected studentsUninfected studentsInfectionWeekly testingLogistic regressionAttack rateConnecticut DepartmentPublic healthViral sourcesViral genome sequencesOutbreakSocial gatheringsAn outbreak of SARS‐CoV‐2 on a transplant unit in the early vaccination era
Roberts SC, Palacios C, Grubaugh ND, Alpert T, Ott IM, Breban MI, Initiative Y, Martinello RA, Smith C, Davis MW, Mcmanus D, Tirmizi S, Topal JE, Azar MM, Malinis M. An outbreak of SARS‐CoV‐2 on a transplant unit in the early vaccination era. Transplant Infectious Disease 2022, 24: e13782. PMID: 34969164, DOI: 10.1111/tid.13782.Peer-Reviewed Original ResearchMeSH KeywordsAntibodies, Monoclonal, HumanizedAntibodies, NeutralizingCOVID-19COVID-19 VaccinesDisease OutbreaksHumansSARS-CoV-2VaccinationConceptsSARS-CoV-2Infection prevention practicesSARS-CoV-2 outbreakTransplant unitCOVID-19-associated morbiditySolid organ transplant recipientsSARS-CoV-2 vaccinationPrevention practicesHospital day 18Potential index casesOrgan transplant recipientsInfection prevention behaviorsMonoclonal antibody therapyCOVID-19SARS-CoV-2 clustersHospital staff membersWhole-genome sequencingAsymptomatic patientsTransplant recipientsPositive patientsAtypical presentationImmunocompromised patientsAntibody therapyVaccination eraDisease progression
2021
Emergence of an early SARS-CoV-2 epidemic in the United States
Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. Cell 2021, 184: 4939-4952.e15. PMID: 34508652, PMCID: PMC8313480, DOI: 10.1016/j.cell.2021.07.030.Peer-Reviewed Original ResearchAsynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic
Petrone ME, Earnest R, Lourenço J, Kraemer MUG, Paulino-Ramirez R, Grubaugh ND, Tapia L. Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic. Nature Communications 2021, 12: 151. PMID: 33420058, PMCID: PMC7794562, DOI: 10.1038/s41467-020-20391-x.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAedesAnimalsChikungunya FeverChikungunya virusChildChild, PreschoolCommunicable Diseases, EmergingDengueDengue VirusDisease OutbreaksDominican RepublicEndemic DiseasesEpidemiological MonitoringFemaleHumansInfantInfant, NewbornMaleMosquito ControlMosquito VectorsSpatio-Temporal AnalysisYoung AdultZika VirusZika Virus InfectionConceptsDengue outbreakDisease outbreaksDengue fever casesOutbreak of chikungunyaMosquito-Borne VirusesFever casesFuture health crisesMosquito-borne disease outbreaksFuture outbreaksVirus transmissionAedes mosquitoesSustainable disease control measuresHealth crisisVirusDisease control measuresOutbreakChikungunyaConstant surveillanceZikaControl measuresDominican Republic
2020
Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors
Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, Coffey LL. Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors. Journal Of Virology 2020, 94: 10.1128/jvi.01605-20. PMID: 32999034, PMCID: PMC7925200, DOI: 10.1128/jvi.01605-20.Peer-Reviewed Original ResearchConceptsCongenital Zika syndromeZika virusFetal infectionFetal deathZika syndromePregnant micePregnant wild-type miceRhesus macaque fetusesPregnant rhesus macaquesZika virus infectionWild-type miceNonpregnant hostsPlacental infectionLow viremiaMajority of animalsPregnant womenPregnant macaquesSevere outcomesMacaque fetusesVirus infectionFetusesInfectionZIKV polyproteinMouse fetusesRhesus macaques
2019
Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks
Pollett S, Fauver JR, Berry I, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. The Journal Of Infectious Diseases 2019, 221: s308-s318. PMID: 31711190, PMCID: PMC11095994, DOI: 10.1093/infdis/jiz302.Peer-Reviewed Original ResearchConceptsGenomic epidemiologyVirus outbreakPublic health responsePublic health toolPublic health agenciesPublic health emergencyKey epidemiological questionsStructured surveillanceChikungunya virusHealth responseEpidemiologyVirus controlHealth toolsHealth agenciesWest NileHealth emergencyVirus genomic dataYellow feverEpidemiological questionsControl of mosquitoesOutbreakOngoing advancesVirus threatsMosquitoesFeverPrecision epidemiology for infectious disease control
Ladner JT, Grubaugh ND, Pybus OG, Andersen KG. Precision epidemiology for infectious disease control. Nature Medicine 2019, 25: 206-211. PMID: 30728537, PMCID: PMC7095960, DOI: 10.1038/s41591-019-0345-2.Peer-Reviewed Original ResearchArbovirus coinfection and co-transmission: A neglected public health concern?
Vogels CBF, Rückert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND. Arbovirus coinfection and co-transmission: A neglected public health concern? PLOS Biology 2019, 17: e3000130. PMID: 30668574, PMCID: PMC6358106, DOI: 10.1371/journal.pbio.3000130.Peer-Reviewed Original ResearchConceptsImpact of coinfectionPublic health concernPublic healthEpidemiological synergyVirus coinfectionAedes aegypti mosquitoesClinical diseaseSuch coinfectionsZika virusCoinfectionOutbreaks of virusesHealth concernAegypti mosquitoesMultiple virusesTransmission dynamicsVirusHealthHumansMosquitoesDiseaseDengue
2018
Tracking virus outbreaks in the twenty-first century
Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG. Tracking virus outbreaks in the twenty-first century. Nature Microbiology 2018, 4: 10-19. PMID: 30546099, PMCID: PMC6345516, DOI: 10.1038/s41564-018-0296-2.Peer-Reviewed Original ResearchMeSH KeywordsCommunicable Diseases, EmergingContact TracingDisease OutbreaksGenome, ViralHumansInformation DisseminationVirusesConceptsWorld Health OrganizationInfectious disease epidemiologyEconomic burdenInfectious diseasesVirus sequencingSubstantial mortalityHealth OrganizationMajor epidemicsUnknown pathogensVirus outbreakDisease epidemiologyPotential causesOutbreak virusesDisease XInitial detectionVirusOutbreakHypothetical outbreakMorbidityCase dataEpidemiologyMortalityDiseaseHuman population
2017
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 2017, 546: 401-405. PMID: 28538723, PMCID: PMC5536180, DOI: 10.1038/nature22400.Peer-Reviewed Original ResearchZika virus evolution and spread in the Americas
Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC. Zika virus evolution and spread in the Americas. Nature 2017, 546: 411-415. PMID: 28538734, PMCID: PMC5563848, DOI: 10.1038/nature22402.Peer-Reviewed Original Research